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ºÜ¶à×öÊäÔ˵ÄͬÐÐÃǶԹ¹½¨Ë«µç¼«ÌåϵµÄ·±ËöºÜ·³ÄÕ¡£ÎÒ֮ǰÊÇÓÃGiew+×Ô¼ºÐ´µÄһЩ½Å±¾À´¹¹½¨Ìåϵ£¬·¢ÏֱȽϷ±Ëö¡£ATKµÄ½çÃæVNL¿ÉÒԽϷ½±ãµÄ¹¹½¨Ìåϵ£¬µ«ÊÇÈç¹û×öÊäÔ˼ÆË㲻ʹÓÃatk¶øÊ¹ÓÃTranSIESTA»òÕßSmeagolµÄ»°£¬ÔõôÀûÓÃVNLÀ´·½±ãµÄ¹¹½¨ÌåÏµÄØ£¿ÏÂÃæÔÛÃǾͿªÊ¼ÌÖÂÛÕâ¸öÎÊÌâ¡£(¿ÉÄÜÒ²»¹ÓÐÆäËûµÄ¸ü¼ò±ãµÄ·½·¨À´¹¹½¨Ìåϵ£¬Ï£ÍûÄÇЩÓÐÆäËû¸ü·½±ã·½·¨À´¹¹½¨ÌåϵµÄͬѧÃǽ«×Ô¼ºµÄ·½·¨·ÖÏíһϡ£) Ê×ÏÈÉùÃ÷£ºÕâ¸ö·½·¨ÒÔ¼°ÏÂÃæÌáµ½µÄ½Å±¾²»ÊÇÎÒ±¾ÈËÔ´´µÄ¡£ÎÒÖ»ÊǸºÔð°ÑËü·Òë³ÉÖÐÎIJ¢ÇÒ×ܽáÁËһ϶øÒÑ¡£ÏêϸµÄÔÌûÇë²Î¿´£ºhttp://quantumwise.com/forum/index.php?topic=5.0 ÏÂÃæµÄʵ¼ù¶¼ÊÇÔÚwindow°æ±¾µÄ2008.10°æ±¾µÄVNLÉÏÃæ²Ù×÷µÄ¡£¶ÔÓÚ±ðµÄ°æ±¾£¬¿ÉÄÜ»áÓÐЩÐí±ä»¯£¬»òÕß²»¿ÉÐУ¬ÐèÒª×Ô¼º³¢ÊÔһϡ£ ************************************************* ¢ÙÊ×ÏÈÔÚwindow°²×°µÄQuantumWise\Virtual NanoLab 2008.10.0\atk\libĿ¼ÏÂÌí¼ÓÒ»¸öĿ¼site-packages ¢Ú½«ÏÂÃæµÄÄÚÈÝ´æÎªÎļþÃûΪxyzexport.pyµÄÎļþ£¬·Åµ½ÉÏÊöĿ¼Ï¡£ ########################## from ATK.KohnSham import * def printXYZFile (configuration): elements = configuration.elements() coordinates = configuration.cartesianCoordinates() print len(elements) print 'From VNL' for elem,coords in zip(elements,coordinates): print elem.symbol(), for i in coords: print i.inUnitsOf(Angstrom), ############################ ¢ÛÔÚVNLÖÐÀûÓÃAtomic Manipulator¹¤¾ß¹¹½¨Ò»¸öË«µç¼«Ìåϵ¡£ ¢ÜÀûÓÃÍ϶¯Í¼±ê½«ÌåϵÍϵ½Script EditorÖУ¬¼ÙÉèÐγɵĽű¾Îª£º ################################ from ATK.TwoProbe import * # Scattering elements left_surface_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold] central_atom_elements = [Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Sulfur, Hydrogen, Hydrogen, Sulfur, Hydrogen, Hydrogen] right_surface_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold] scattering_elements = left_surface_elements + central_atom_elements + right_surface_elements # Scattering coordinates left_surface_coordinates = [[ 0.00000000e+00, 0.00000000e+00, 7.06330299e+00], [ -1.44179070e+00, 2.49725485e+00, 7.06330299e+00], [ -2.88358140e+00, 4.99450970e+00, 7.06330299e+00], [ 2.88358140e+00, 0.00000000e+00, 7.06330299e+00], [ 1.44179070e+00, 2.49725485e+00, 7.06330299e+00], [ 0.00000000e+00, 4.99450970e+00, 7.06330299e+00], [ 5.76716280e+00, 0.00000000e+00, 7.06330299e+00], [ 4.32537222e+00, 2.49725485e+00, 7.06330299e+00], [ 2.88358140e+00, 4.99450970e+00, 7.06330299e+00], [ -2.88358140e+00, 6.65934610e+00, 9.41773796e+00], [ 0.00000000e+00, 1.66483653e+00, 9.41773796e+00], [ -1.44179070e+00, 4.16209126e+00, 9.41773796e+00], [ 1.33226763e-15, 6.65934610e+00, 9.41773796e+00], [ 2.88358140e+00, 1.66483653e+00, 9.41773796e+00], [ 1.44179070e+00, 4.16209126e+00, 9.41773796e+00], [ 2.88358140e+00, 6.65934610e+00, 9.41773796e+00], [ 5.76716280e+00, 1.66483653e+00, 9.41773796e+00], [ 4.32537222e+00, 4.16209126e+00, 9.41773796e+00]]*Angstrom central_atom_coordinates = [[ 1.44 , 2.5 , 15.68600003], [ 1.44 , 1.29100001, 14.98800001], [ 1.44 , 1.29100001, 13.59199999], [ 1.44 , 2.5 , 12.89399997], [ 1.44 , 3.70899999, 13.59199999], [ 1.44 , 3.70899999, 14.98800001], [ 1.44 , 2.5 , 17.4400001 ], [ 1.44 , 0.35299993, 15.53000001], [ 1.44 , 0.35299993, 13.04999999], [ 1.44 , 2.5 , 11.1399999 ], [ 1.44 , 4.64700007, 13.04999999], [ 1.44 , 4.64700007, 15.53000001]]*Angstrom right_surface_coordinates = [[ -2.88358140e+00, 6.65934610e+00, 1.91477375e+01], [ 0.00000000e+00, 1.66483653e+00, 1.91477375e+01], [ -1.44179070e+00, 4.16209126e+00, 1.91477375e+01], [ 1.33226763e-15, 6.65934610e+00, 1.91477375e+01], [ 2.88358140e+00, 1.66483653e+00, 1.91477375e+01], [ 1.44179070e+00, 4.16209126e+00, 1.91477375e+01], [ 2.88358140e+00, 6.65934610e+00, 1.91477375e+01], [ 5.76716280e+00, 1.66483653e+00, 1.91477375e+01], [ 4.32537222e+00, 4.16209126e+00, 1.91477375e+01], [ -1.44179070e+00, 5.82692766e+00, 2.15021718e+01], [ 1.44179070e+00, 8.32418263e-01, 2.15021718e+01], [ 0.00000000e+00, 3.32967305e+00, 2.15021718e+01], [ 1.44179070e+00, 5.82692766e+00, 2.15021718e+01], [ 4.32537222e+00, 8.32418263e-01, 2.15021718e+01], [ 2.88358140e+00, 3.32967305e+00, 2.15021718e+01], [ 4.32537222e+00, 5.82692766e+00, 2.15021718e+01], [ 7.20895386e+00, 8.32418263e-01, 2.15021718e+01], [ 5.76716280e+00, 3.32967305e+00, 2.15021718e+01]]*Angstrom scattering_coordinates = left_surface_coordinates + central_atom_coordinates + right_surface_coordinates electrode_elements = [Gold, Gold, Gold] electrode_coordinates = [[ 0.00000000e+00, 0.00000000e+00, 0.00000000e+00], [ 1.11022302e-16, 1.66483653e+00, 2.35443440e+00], [ 1.44179073e+00, 8.32418264e-01, 4.70886880e+00]]*Angstrom electrode_cell = [[ 2.88358145, 0. , 0. ], [-1.44179073, 2.49725479, 0. ], [ 0. , 0. , 7.06330319]]*Angstrom # Set up electrodes electrode_configuration = PeriodicAtomConfiguration( electrode_cell, electrode_elements, electrode_coordinates ) # Set up two-probe configuration twoprobe_configuration = TwoProbeConfiguration( (electrode_configuration,electrode_configuration), scattering_elements, scattering_coordinates, electrode_repetitions=[[3,3],[3,3]], equivalent_atoms=([0,0],[-1,-1]) ) #################################### ÔÚ´°¿ÚÖУ¬Ôڽű¾×îºóÌí¼ÓÁ½ÐУº from xyzexport import printXYZFile printXYZFile(twoprobe_configuration.equivalentBulkSystem()) ¢ÝÈ»ºóÍÏÈëJob Manager¹¤¾ßÖУ¬ÔÚlogWindowÖлá³öÏÖxyz¸ñʽµÄ½á¹¹¡£ Èç¹û½ö½öÏëµÃµ½À©Õ¹·Ö×ӽṹ¶ø²»ÏëµÃµ½´ø×óÓҵ缫µÄË«µç¼«Ìåϵ£¬ÄÇô½«¢ÜÖеĵڶþÐл»³É£º printXYZFile(twoprobe_configuration) ¼´¿É¡£ Èç¹ûÄãÏëת»»µÄÌåϵ²»ÊÇË«µç¼«Ìåϵ¶øÊDZðµÄÌåϵ£¬ÄÇô printXYZFile(twoprobe_configuration) ÖеĶÔÏó»»³ÉÄã½Å±¾ÖÐÏàÓ¦µÄ¶ÔÏóÃû³Æ¡£ ×¢£ºÈç¹ûÓÃÉÏÃæµÄ·½·¨¿ÉÄܵõ½µÄË«µç¼«Ìåϵ²»ÊǺÜÃÀ¹Û£¬·¢ÏÖ×óÓÒÁ½¸öµç¼«²Î²î²»Æë£¬Õâ¸öʱºò£¬ ¿ÉÒÔÔÚ¢Û½¨Á¢ºÃË«µç¼«Ìåϵ֮ºó£¬ÀûÓÃ"Save Equivalent bulk configuration to file"Ñ¡Ï½«Ìåϵ´æÎªbulkÌåϵ£¬ È»ºó½øÐÐ¢Ü ÒÔºóÔÙʹÓõÄʱºò¾Í¿ÉÒÔÊ¡ÂÔ¢Ù¢Ú²½ÁË¡£ ************************************************* Ï£ÍûÉÏÊö·½·¨Äܹ»°ïÖúÄÇЩƽʱÀûÓÃSmeagolºÍTranSIESTA×ö¼ÆËãµÄÄÇЩͬ־Ãǹ¹½¨Ìåϵ¡£ [ Last edited by zhangguangping on 2011-7-31 at 12:05 ] |
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